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Genomic Sequence Diversity and Population Structure of Saccharomyces cerevisiae Assessed by RAD-seq
The budding yeast Saccharomyces cerevisiae is important for human food production and as a model organism for biological research. The genetic diversity contained in the global population of yeast strains represents a valuable resource for a number of fields, including genetics, bioengineering, and...
Autores principales: | , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Genetics Society of America
2013
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3852379/ https://www.ncbi.nlm.nih.gov/pubmed/24122055 http://dx.doi.org/10.1534/g3.113.007492 |
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author | Cromie, Gareth A. Hyma, Katie E. Ludlow, Catherine L. Garmendia-Torres, Cecilia Gilbert, Teresa L. May, Patrick Huang, Angela A. Dudley, Aimée M. Fay, Justin C. |
author_facet | Cromie, Gareth A. Hyma, Katie E. Ludlow, Catherine L. Garmendia-Torres, Cecilia Gilbert, Teresa L. May, Patrick Huang, Angela A. Dudley, Aimée M. Fay, Justin C. |
author_sort | Cromie, Gareth A. |
collection | PubMed |
description | The budding yeast Saccharomyces cerevisiae is important for human food production and as a model organism for biological research. The genetic diversity contained in the global population of yeast strains represents a valuable resource for a number of fields, including genetics, bioengineering, and studies of evolution and population structure. Here, we apply a multiplexed, reduced genome sequencing strategy (restriction site−associated sequencing or RAD-seq) to genotype a large collection of S. cerevisiae strains isolated from a wide range of geographical locations and environmental niches. The method permits the sequencing of the same 1% of all genomes, producing a multiple sequence alignment of 116,880 bases across 262 strains. We find diversity among these strains is principally organized by geography, with European, North American, Asian, and African/S. E. Asian populations defining the major axes of genetic variation. At a finer scale, small groups of strains from cacao, olives, and sake are defined by unique variants not present in other strains. One population, containing strains from a variety of fermentations, exhibits high levels of heterozygosity and a mixture of alleles from European and Asian populations, indicating an admixed origin for this group. We propose a model of geographic differentiation followed by human-associated admixture, primarily between European and Asian populations and more recently between European and North American populations. The large collection of genotyped yeast strains characterized here will provide a useful resource for the broad community of yeast researchers. |
format | Online Article Text |
id | pubmed-3852379 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2013 |
publisher | Genetics Society of America |
record_format | MEDLINE/PubMed |
spelling | pubmed-38523792013-12-06 Genomic Sequence Diversity and Population Structure of Saccharomyces cerevisiae Assessed by RAD-seq Cromie, Gareth A. Hyma, Katie E. Ludlow, Catherine L. Garmendia-Torres, Cecilia Gilbert, Teresa L. May, Patrick Huang, Angela A. Dudley, Aimée M. Fay, Justin C. G3 (Bethesda) Investigations The budding yeast Saccharomyces cerevisiae is important for human food production and as a model organism for biological research. The genetic diversity contained in the global population of yeast strains represents a valuable resource for a number of fields, including genetics, bioengineering, and studies of evolution and population structure. Here, we apply a multiplexed, reduced genome sequencing strategy (restriction site−associated sequencing or RAD-seq) to genotype a large collection of S. cerevisiae strains isolated from a wide range of geographical locations and environmental niches. The method permits the sequencing of the same 1% of all genomes, producing a multiple sequence alignment of 116,880 bases across 262 strains. We find diversity among these strains is principally organized by geography, with European, North American, Asian, and African/S. E. Asian populations defining the major axes of genetic variation. At a finer scale, small groups of strains from cacao, olives, and sake are defined by unique variants not present in other strains. One population, containing strains from a variety of fermentations, exhibits high levels of heterozygosity and a mixture of alleles from European and Asian populations, indicating an admixed origin for this group. We propose a model of geographic differentiation followed by human-associated admixture, primarily between European and Asian populations and more recently between European and North American populations. The large collection of genotyped yeast strains characterized here will provide a useful resource for the broad community of yeast researchers. Genetics Society of America 2013-10-11 /pmc/articles/PMC3852379/ /pubmed/24122055 http://dx.doi.org/10.1534/g3.113.007492 Text en Copyright © 2013 Cromie et al. http://creativecommons.org/licenses/by/3.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution Unported License (http://creativecommons.org/licenses/by/3.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Investigations Cromie, Gareth A. Hyma, Katie E. Ludlow, Catherine L. Garmendia-Torres, Cecilia Gilbert, Teresa L. May, Patrick Huang, Angela A. Dudley, Aimée M. Fay, Justin C. Genomic Sequence Diversity and Population Structure of Saccharomyces cerevisiae Assessed by RAD-seq |
title | Genomic Sequence Diversity and Population Structure of Saccharomyces cerevisiae Assessed by RAD-seq |
title_full | Genomic Sequence Diversity and Population Structure of Saccharomyces cerevisiae Assessed by RAD-seq |
title_fullStr | Genomic Sequence Diversity and Population Structure of Saccharomyces cerevisiae Assessed by RAD-seq |
title_full_unstemmed | Genomic Sequence Diversity and Population Structure of Saccharomyces cerevisiae Assessed by RAD-seq |
title_short | Genomic Sequence Diversity and Population Structure of Saccharomyces cerevisiae Assessed by RAD-seq |
title_sort | genomic sequence diversity and population structure of saccharomyces cerevisiae assessed by rad-seq |
topic | Investigations |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3852379/ https://www.ncbi.nlm.nih.gov/pubmed/24122055 http://dx.doi.org/10.1534/g3.113.007492 |
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